Mapping Heat Resistance in YeastsIn a proof-of-concept study, researchers demonstrated that a new genetic mapping strategy called RH-Seq can identify genes that promote heat resistance in the yeast Saccharomyces cerevisiae, allowing this species to grow better than its closest relative S. paradoxus at high temperatures.

First Monoploid Reference Sequence of SugarcaneFor the highly polyploid sugarcane, an international team of researchers has successfully assembled a first monoploid reference sequence using a targeted approach that focused on the gene rich part of the genome by harnessing information from a sequenced related species – sorghum.

Defining a Pan-Genome for Antarctic ArchaeaSome Antarctic lakes have salinities 10 times that of seawater. By collecting and sequencing dominant haloarchaeal sequences from six hypersaline lakes, researchers focused on understanding the genomic variation in haloarchaea across East Antarctica.

Methane Flux in the AmazonWetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.

Insights into Functional Diversity in NeurosporaThis proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.

Mining IMG/M for CRISPR-Associated ProteinsResearchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.

DAS Tool for Genome Reconstruction from MetagenomesThrough the JGI’s Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. The work was published in Nature Microbiology.

Preparing for a Sequence Data DelugeThe approved CSP 2019 proposals leverage new capabilities and higher throughput in DNA sequencing, synthesis and metabolomics. Additionally, just over half of the accepted proposals come from primary investigators who have never led any previously accepted JGI proposal.

Innovative Technology Improves Our Understanding of Bacterial Cell SignalingCyclic di-GMP (Guanine Monophosphate) is found in nearly all types of bacteria and interacts with cell signaling networks that control many basic cellular functions. To better understand the dynamics of this molecule, researchers developed the first chemiluminescent biosensors for measuring cyclic di-GMP in bacteria through work enabled by the JGI’s Community Science Program (CSP).

Hidden Giants in Forest SoilsIn Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. Most of the genomes were uncovered using a "mini-metagenomics" approach that reduced the complexity of the soil microbial communities sequenced and analyzed.

Symbiosis a Driver of Truffle DiversityTruffles are the fruiting bodies of the ectomycorrhizal (ECM) fungal symbionts residing on host plant roots. In Nature Ecology & Evolution, an international team sought insights into the ECM lifestyle of truffle-forming species. They conducted a comparative analysis of eight Pezizomycete fungi, including four species prized as delicacies.

Expanding Fungal Diversity, One Cell at a TimeIn Nature Microbiology, a team led by JGI researchers has developed a pipeline to generate genomes from single cells of uncultivated fungi. The approach was tested on several uncultivated fungal species representing early diverging fungi.

Charting Short-Term Results of Wetlands Restoration

Patterns in carbon sequestration and emissions are charted in the San Joaquin Delta.

The Science:

Researchers at the DOE Joint Genome Institute sequenced and analyzed the microbial communities in restored wetlands in the Sacramento-San Joaquin Delta and combined the data with greenhouse gas measurements from the area to track patterns in methane emissions.

After a day collecting samples from Twitchell Island, located in the Sacramento-San Joaquin Delta of California, USGS scientist and study co-author Lisamarie Windham-Myers (left), study senior author Susannah Tringe (center), and study first author Shaomei He (right) go over their preliminary findings. (Image by David Gilbert, DOE JGI). A video about the project can be viewed here.

The Impact:

Though wetlands account for less than 10 percent of the planet’s land surface area, they trap as much as 30 percent of global soil carbon. In addition, natural wetlands can emit nearly 40 percent of global methane emissions. Determining if restored wetlands could serve as carbon sinks or act as carbon emitters is a key goal of the project.

Summary

In the late 19th and early 20th century, several freshwater tidal marshes in California’s Sacramento-San Joaquin Delta were drained and converted for agricultural purposes. A century later, the U.S. Geological Survey (USGS) and the California Department of Water Resources launched a pilot project focused on Twitchell Island to restore these wetlands for a number of reasons, including the mitigation of levee failure, land surface subsidence and erosion.

Wetlands cover less than 10 percent of the Earth’s land surface, but they can trap as much as 30 percent of global soil carbon, as well as emit nearly 40 percent of global methane emissions. Before agencies can consider long-term wetland restoration projects, they want to learn more about whether or not restored wetlands can serve as carbon sinks or act as carbon emitters.

In a study published May 19, 2015 in the journal mBio, a team led by Susannah Tringe, head of the Metagenome Program at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility managed by Lawrence Berkeley National Laboratory, reported on microbial community composition and carbon emissions patterns from data collected at different times, from Twitchell Island sites near the inlet and leading toward the interior of the wetland.

The team collected an abundance of data relating to microbial community composition and greenhouse gas emissions. DNA collected from the soil samples was sequenced and analyzed at the DOE JGI. One of the team’s findings was that the microbial communities present in the restored wetlands were more diverse than the composition of the microbial communities in an adjacent cornfield. Additionally, the river water became slightly more acidic as it moved from the river inlet toward the wetland interior, likely due to the decomposing plant mass found “inland.” A similar pattern was observed regarding the methane emissions, with lower emissions detected at the inlet compared to the interior sites.

DOE JGI Metagenome Program Head Susannah Tringe and postdoc Susie Theroux discuss the lessons to be learned from studying the microbial diversity of marshes that have been converted to other uses, and are now being restored, as well as the potential impacts on the global carbon cycle. Watch the video at http://bit.ly/JGI15CCMarshes.

“The differences in microbial community composition and functional profiles reveal complex interactions among functional guilds and among wetland plants, microorganisms and their environment,” the team reported. “Based on these findings, more specific studies can be carried out to evaluate the impact of wetland water chemistry and hydrology on CH4 emission and carbon sequestration before large-scale restoration projects are implemented.”